Special Issue Information

Dear Colleagues,

The advent of powerful analytic techniques, such as pulsed laser polymerization (PLP) combined with size exclusion chromatography (SEC), has enabled the reliable and accurate estimation of propagation rate coefficients in free radical polymerization (FRP). However, the measurement of kinetic parameters, such as activation energies and rate coefficients, is time consuming and complicated by difficult experimental conditions as well as secondary reaction mechanisms that occur simultaneously. As a result, it is often impossible to focus on individual contributions in isolation from the whole kinetic scheme. On the other hand, Computational Chemistry can be used to elucidate mechanisms and reaction pathways to complement experimental analyses. In fact, the rapid and continual increase in computer power has enabled the combination of Quantum Chemistry, Semiempirical Methods, and Molecular Dynamics to determine with satisfactory accuracy different properties such as molecular geometries (bond lengths, bond angles, and torsional angles), energetic reaction profiles, vibrational frequencies of molecular species, transition state structures, and reaction frequency factors.

Prof. Dr. Davide MoscatelliGuest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed Open Access monthly journal published by MDPI.

Abstract: Proteins are heteropolymers that play important roles in virtually every biological reaction. While many proteins have well-defined three-dimensional structures that are inextricably coupled to their function, intrinsically disordered proteins (IDPs) do not have a well-defined structure, and it is this lack of structure that facilitates their function. As many IDPs are involved in essential cellular processes, various diseases have been linked to their malfunction, thereby making them important drug targets. In this review we discuss methods for studying IDPs and provide examples of how computational methods can improve our understanding of IDPs. We focus on two intensely studied IDPs that have been implicated in very different pathologic pathways. The first, p53, has been linked to over 50% of human cancers, and the second, Amyloid-β (Aβ), forms neurotoxic aggregates in the brains of patients with Alzheimer’s disease. We use these representative proteins to illustrate some of the challenges associated with studying IDPs and demonstrate how computational tools can be fruitfully applied to arrive at a more comprehensive understanding of these fascinating heteropolymers.

Abstract: Recent progress of simulations/modeling at the atomic level has led to a better understanding of the mechanical behaviors of graphene, which include the linear elastic modulus E, the nonlinear elastic modulus D, the Poisson’s ratio ν, the intrinsic strength σint and the corresponding strain εint as well as the ultimate strain εmax (the fracture strain beyond which the graphene lattice will be unstable). Due to the two-dimensional geometric characteristic, the in-plane tensile response and the free-standing indentation response of graphene are the focal points in this review. The studies are based on multiscale levels: including quantum mechanical and classical molecular dynamics simulations, and parallel continuum models. The numerical studies offer useful links between scientific research with engineering application, which may help to fulfill graphene potential applications such as nano sensors, nanotransistors, and other nanodevices.

Abstract: Collagen molecules are the primary structural proteins of many biological systems. Much progress has been made in the study of the structure and function of collagen, but fundamental understanding of its electronic structures at the atomic level is still lacking. We present the results of electronic structure and bonding calculations of a specific model of type I collagen using the density functional theory-based method. Information on density of states (DOS), partial DOS, effective charges, bond order values, and intra- and inter-molecular H-bonding are obtained and discussed. We further devised an amino-acid-based potential method (AAPM) to circumvent the full self-consistent field (SCF) calculation that can be applied to large proteins. The AAPM is validated by comparing the results with the full SCF calculation of the whole type I collagen model with three strands. The calculated effective charges on each atom in the model retained at least 95% accuracy. This technique provides a viable and efficient way to study the electronic structure of large complex biomaterials at the ab initio level.

Planned Papers

The below list represents only planned manuscripts. Some of these
manuscripts have not been received by the Editorial Office yet. Papers
submitted to MDPI journals are subject to peer-review.

Type of Paper: ReviewTitle: An overview on the Structure-Reactivity Relationship and the Solvent Effect in the Free-Radical Polymerization of Acrylate Derivatives: A DFT StudyAuthors: Özlem Karahan and Viktorya AviyenteAffiliation: Department of Chemistry, Bogazici University Abstract: Alkyl α-hydroxymethacrylate (RHMA) derivatives (A1-A3) known to polymerize efficiently via free radical polymerization have been modeled. The long range C=O…H-C interactions are found to stabilize the transition structures of the dimeric units chosen as models. Similarly, the reactivity of acrylate derivatives (A4, A5 and A6) has been attributed to the presence of C=O…H-C, C=O…H-Ф and π-π stabilizing interactions, respectively. A quantitative structure-activity relationship with B3LYP/6-31+G* was generated with quantum chemical descriptors for 16 alkyl α-hydroxymethacrylate (RHMA) monomers. In the next part of this study, the effect of methanol as a solvent in the polymerization rate and the tacticity of poly(N-Isopropylacrylamide) (PNIPAM) is studied with hybrid computational tools. In the last part of this review, the propagation rate of EHMA in ethanol and toluene has been investigated with the MPW1K/6-311+G(3df,2p)//B3LYP/6-31+G(d) methodology.